Journal ArticleDOI
Reuse of public genome-wide gene expression data
Johan Rung,Alvis Brazma +1 more
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TLDR
The utility of the gene expression data that are in the public domain and how researchers are making use of these data are discussed and recommendations are provided that can improve the utility of such data.Abstract:
Our understanding of gene expression has changed dramatically over the past decade, largely catalysed by technological developments. High-throughput experiments - microarrays and next-generation sequencing - have generated large amounts of genome-wide gene expression data that are collected in public archives. Added-value databases process, analyse and annotate these data further to make them accessible to every biologist. In this Review, we discuss the utility of the gene expression data that are in the public domain and how researchers are making use of these data. Reuse of public data can be very powerful, but there are many obstacles in data preparation and analysis and in the interpretation of the results. We will discuss these challenges and provide recommendations that we believe can improve the utility of such data.read more
Citations
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Proceedings ArticleDOI
EZLearn: Exploiting Organic Supervision in Automated Data Annotation
TL;DR: Without using any manually labeled data, the EZLearn system learned to accurately annotate data samples in functional genomics and scientific figure comprehension, substantially outperforming state-of-the-art supervised methods trained on tens of thousands of annotated examples.
Journal ArticleDOI
Compartmentalization of Intrarenal Programmed Cell Death Protein 1-Ligand 1 and Its Receptor in Kidney Injury Related to Immune Checkpoint Inhibitor Nephrotoxicity
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Dissertation
Computational Curation of Open Science Data
TL;DR: Computational Curation of Open Science Data is presented as a probabilistic procedure to estimate the probability that a particular type of data will be chosen for an particular science research project.
Posted ContentDOI
Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing
Gabriella Rustici,Eleanor Williams,Mitra Barzine,Alvis Brazma,Roger E. Bumgarner,Marco Chierici,Cesare Furlanello,Liliana Greger,Giuseppe Jurman,Michael Miller,B. F. Francis Ouellette,John Quackenbush,Michael R. Reich,Christian J. Stoeckert,Ronald C. Taylor,Stephen Chervitz Trutane,Jennifer B. Weller,Brian T. Wilhelm,Neil Winegarden +18 more
TL;DR: In this paper, the authors present a historical snapshot of the data sharing situation focusing on transcriptomics data from both microarray and RNA-sequencing experiments published between 2009 and 2013, a period during which RNA-seq studies became increasingly popular for transcriptome analysis.
References
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